Yep, their stock can stain them in some cases. My Mir came out of her box with light staining, and I know there's a Dal who is always badly stained out of her box (but I can't recall who it is). I know there's a way to treat the clothes that helps keep them from staining your dolls further, but I can't remember what it is.
Edit; Missed your second question. xD
All three of my Pullips are still on their stock bodies. I have no trouble posing them or having them sit down without falling, but I know Ala has a weak forearm and can't hold one of them up. When leaning against something man can stand pretty decently too. But I've never worked with an Obitsu body before so I can't tell you if that's a better choice.